Janet Ouko accuses the governor of uttering false and malicious words indicating that she should be held to account for the loss.
Sonko made the remarks at a press conference on January 9 in Mombasa.
"As the head of the docket, the county government lost Sh 357 million for which she is to be held to account. We wrote cheques to schools but the same were secretly brought back, cancelled and fresh ones written to their cronies names," Ouko quotes Sonko in her affidavit.
In the affidavit filed on Thursday evening, Ouko said the words were understood to mean that she is a forger, corrupt, unreliable, incompetent, professionally and morally unfit for any employment and association.
She alleged Sonko made the statement "in full knowledge that the allegations are untrue".
"The utterances and publication which was read and seen by millions of people was malicious, oppressive and spiteful which was calculated to injure and lower the self-esteem with which members of the local and international society regarded and held me," Ouko said.
The Ex-CEC said she continues to suffer injuries in character and reputation as a consequence of the words of the governor.
Ouko said she has been brought to grave public ridicule, hatred, scandal and contempt in the society.
She said even after she wrote a demand notice of apology to the governor, Sonko still went ahead and uttered that he had reported the alleged loss of the money to the DCI, DPP and EACC.
She said this triggered an uproar on social media portraying her as a thief who pilfered money meant for poor school children.
Ouko wants the court to order Sonko to apologise and a retraction of similar prominence as the defamatory words be made.
She also wants to be paid general damages for libel and malicious falsehood as well as exemplary damages and damages for psychological and emotional distress.
Ouko resigned from her post on January 7 and two days later, Sonko linked her to the loss of millions at the county.